Could we write to them as a community? As the 'CCP4 Peer Reviewing Organisation for Structural Biology'?
Great job indeed! Cheers, leo - Leonard Chavas - Synchrotron SOLEIL Proxima-I L'Orme des Merisiers Saint-Aubin - BP 48 91192 Gif-sur-Yvette Cedex France - Phone: +33 169 359 746 Mobile: +33 644 321 614 E-mail: leonard.cha...@synchrotron-soleil.fr - > On 09 Sep 2016, at 13:39, Manfred S. Weiss > <manfred.we...@helmholtz-berlin.de> wrote: > > > Good job Randy! > > Now, in order to finish this off properly somebody should > refine the structure, alert the editor of the journal as well > as the corresponding author of the paper. > > If we leave it at that, the only thing we have is the satisfaction > that we managed to "peer review" this structure, but nothing else is > going to happen. > > Cheers, Manfred > > > On 09.09.2016 13:34, Gerard Bricogne wrote: >> Dear Randy, >> >> Congratulations for this terrific piece of work! >> >> As James Fraser was writing two days ago, this case establishes a >> new paradigm for the "peer review" of structural papers :-) . >> >> >> With best wishes, >> >> Gerard. >> >> -- >> On Fri, Sep 09, 2016 at 12:20:53PM +0100, Randy Read wrote: >>> Dear all, >>> >>> Following on from Paul’s suggestion that the space group is wrong, I >>> thought it might be interesting to try to solve this structure from >>> scratch, using what I’m currently teaching students at a CCP4 workshop. >>> What worked was to find some distant homologues with HHpred (top 3 hits >>> after ignoring 5gnn), make a trimmed ensemble, and search with that. This >>> gave a very clear solution for one molecule in P65. Model completion from >>> that point works really well, given the resolution, using either >>> phenix.autobuild or ARP/wARP. >>> >>> For the edification of the members of the BB, the ARP/wARP model is >>> attached! (Hopefully no flames for an attachment of 135kB…) This model >>> hasn’t had some really obvious rotamer fixes or extensions of the termini >>> applied, but it has good stereochemistry, and R/Rfree are 0.241/0.285. >>> >>> Given the vastly improved statistics for a different space group and the >>> huge differences in the model, it is to be hoped that the authors retract >>> the original publication and PDB entry. Thanks to Gerard for pointing out >>> the issues with this! >>> >>> Best wishes, >>> >>> Randy Read >>> >> >> >>> >>> >>> ----- >>> Randy J. Read >>> Department of Haematology, University of Cambridge >>> Cambridge Institute for Medical Research Tel: +44 1223 336500 >>> Wellcome Trust/MRC Building Fax: +44 1223 336827 >>> Hills Road >>> E-mail: rj...@cam.ac.uk >>> Cambridge CB2 0XY, U.K. >>> www-structmed.cimr.cam.ac.uk >>> >>>> On 7 Sep 2016, at 16:51, Paul Adams <pdad...@lbl.gov> wrote: >>>> >>>> Dear Gerard, >>>> >>>> thanks for pointing this structure out. This is indeed very startling. The >>>> paper indicates that the structure was refined with Phenix. However, if I >>>> download the model/data and refine (with Phenix) the starting R-factors >>>> are 0.36/0.38 and these get worse during refinement. Clearly the deposited >>>> model is not consistent with the R-factors reported in the paper, or in >>>> the wwPDB. In addition, analysis of the data suggests strongly that the >>>> true symmetry is P6 (possibly with a screw axis) - I suspect that this is >>>> the genesis of statements about twinning, but it isn’t clear if that was >>>> used in the refinement. Being charitable I can imagine that the wrong >>>> model was deposited in the wwPDB. However, this doesn’t explain the >>>> R-factors reported by the wwPDB, or the less than convincing images of the >>>> structure shown in the paper. I very much agree with you that there must >>>> have been ample alarms sounded along the way. It is cautionary that this >>>> wasn’t caught at some point. For me this highlights that the issues go >>>> beyond the naivety or impatience of a single student. >>>> >>>> Cheers, >>>> Paul >>>> >>>>> On Sep 7, 2016, at 7:20 AM, Gerard Bricogne <g...@globalphasing.com> >>>>> wrote: >>>>> >>>>> Dear all, >>>>> >>>>> While the thread on "Another MR pi(t)fall" is still lukewarm, and >>>>> the discussion it triggered hopefully still present in readers' minds, >>>>> I would like to bring another puzzling entry to the BB's attention. >>>>> >>>>> When reviewing on Monday the weekend's BUSTER runs on the last >>>>> batch of PDB depositions, Andrew Sharff (here) noticed that entry 5gnn >>>>> had been flagged as giving much larger R-values when re-refined with >>>>> BUSTER (0.3590/0.3880) than the deposited ones (0.2210/0.2500). This >>>>> led us to carry out some investigation of that entry. >>>>> >>>>> The deposited coordinates were flagged by BUSTER as having 4602 >>>>> bond-length violations, the worst being 205.8 sigmas, and other wild >>>>> outliers. The initial Molprobity analysis gave a clash score of near >>>>> 100, placing it in the 0-th percentile. The PDB validation report is >>>>> dominantly red and ochre, with only a few wisps of green. >>>>> >>>>> Examining the model and map with Coot showed "waters, waters >>>>> everywhere", disconnected density, and molecules separated by large >>>>> layers of water. The PDB header lists hundreds of water molecules in >>>>> REMARK 525 records that are further than 5.0 Angs from the nearest >>>>> chain, some of them up to 15 Angs away. >>>>> >>>>> The cartoons on the NCBI server at >>>>> >>>>> http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=142582&dps=1 >>>>> >>>>> show random coils threaded up and down through beta-strands, and the >>>>> one on the RCSB PDB site at >>>>> >>>>> http://www.rcsb.org/pdb/explore.do?structureId=5GNN >>>>> >>>>> also shows mostly random coil, with only very few and very short >>>>> segments of secondary structure. >>>>> >>>>> In reciprocal space, an oddness of a different kind is that if >>>>> one looks at the mtz file, the amplitudes and their sigmas are on a >>>>> very small scale. However the STARANISO display shows a smooth and >>>>> plausible distribution of I/sig(I) to the full nominal resolution >>>>> limit of 1.6A. >>>>> >>>>> Looking at the publication associated with this entry >>>>> >>>>> http://www.ncbi.nlm.nih.gov/pubmed/27492925 >>>>> >>>>> indicates that the structure was solved by MR from a model obtained >>>>> from a structure prediction server (I-TASSER). No further details are >>>>> given, even in the Supplemental Material. Table 1 does report a >>>>> MolProbity clash score of 103.59, as well as 10% Ramachandran outliers >>>>> and 25.51% rotamer outliers. It also contains a mention of a twinning >>>>> operator -h, -k, l with a twinning fraction of 0.5, although there is >>>>> no mention of it in the text nor in the PDB file. >>>>> >>>>> I will follow my own advice and resist the temptation of calling >>>>> this "the end of civilisation as we know it", but this is startling. >>>>> Perhaps we have over-advertised to the non-experts the few successes >>>>> of structure prediction programs as reliable sources of MR models and >>>>> thus created unwarranted optimism, besides the usual exaggeration of >>>>> the degree to which X-ray crystallography has become a push-button >>>>> commodity that can deliver results to untrained users. What is also >>>>> disconcerting is that the abundant alarm bells that rang along the way >>>>> (the MolProbity clash score and geometry reports, the contents of the >>>>> PDB validation report, and simple common sense when examining electron >>>>> density and model) failed to make anyone involved along the way take >>>>> notice that there was something seriously wrong. >>>>> >>>>> This case seems to bring to the forefront even more vividly than >>>>> 4nl6 and 4nl7 some collective issues that we face. Here the problem is >>>>> not one of contamination of a protein prep resulting in crystals of >>>>> "the wrong protein": there is also a more diffuse contamination by >>>>> deficiencies of judgement, expertise and vigilance at several >>>>> consecutive stages, including refereeing and publication. >>>>> >>>>> Validation is a hot topic at the moment, and this may serve as a >>>>> concrete example that some joined-up thinking and action is indeed a >>>>> matter of urgency, and that extreme scenarios of things going wrong do >>>>> not exist solely in the imaginations of obsessive-compulsive/paranoid >>>>> validators. >>>>> >>>>> I am grateful to several colleagues for correspondance and >>>>> discussions on the matters touched upon on this message. >>>>> >>>>> >>>>> With best wishes, >>>>> >>>>> Gerard >>>>> >>>>> -- >>>>> >>>>> =============================================================== >>>>> * * >>>>> * Gerard Bricogne g...@globalphasing.com * >>>>> * * >>>>> * Global Phasing Ltd. * >>>>> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * >>>>> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * >>>>> * * >>>>> =============================================================== >>>> >>>> -- >>>> Paul Adams >>>> Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence >>>> Berkeley Lab >>>> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley >>>> Lab >>>> Adjunct Professor, Department of Bioengineering, U.C. Berkeley >>>> Vice President for Technology, the Joint BioEnergy Institute >>>> Laboratory Research Manager, ENIGMA Science Focus Area >>>> >>>> Building 33, Room 347 >>>> Building 80, Room 247 >>>> Building 978, Room 4126 >>>> Tel: 1-510-486-4225, Fax: 1-510-486-5909 >>>> http://cci.lbl.gov/paul >>>> >>>> Lawrence Berkeley Laboratory >>>> 1 Cyclotron Road >>>> BLDG 33R0345 >>>> Berkeley, CA 94720, USA. >>>> >>>> Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 >>>> ] >>>> -- > > -- > Dr. Manfred. S. Weiss > Helmholtz-Zentrum Berlin für Materialien und Energie > Macromolecular Crystallography (HZB-MX) > Albert-Einstein-Str. 15 > D-12489 Berlin > GERMANY > Fon: +49-30-806213149 > Fax: +49-30-806214975 > Web: http://www.helmholtz-berlin.de/bessy-mx > Email: mswe...@helmholtz-berlin.de > > ________________________________ > > Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren > e.V. > > Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. > Jutta Koch-Unterseher > Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de
